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Hello freesurfer experts,
I would like to use freesurfer recon-all to obtain the regional cortical thicknesses of subjects of ADNI dataset. I launched freesurfer recon-all and obtained the parcellations according to Destrieux and Desikan-Killiany atlases. I would like to know how to obtain the same parcellations with another atlas, AICHA (https://secure-web.cisco.com/1st38nLf-34KvmX5j8oNCBRhTI_Ki20PWEfeEACfqaaGqdi...), which is only available in nifti format.
I understood that I should create a .gcs file from the nifti version but I am not sure how. I saw that mris_ca_train could be used to create such a file from a a manually labelled dataset but I don’t know how to create these labelled subjects from the nifti atlas.
If anyone has already this kind of conversion .nii -> .gcs I would be really interested to know how you have done that!
Best regards, Elina